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Source Code for Biology and Medicine, Volume 9
Volume 9, 2014
- David Campos, Quoc-Chinh Bui, Sérgio Matos
, José Luís Oliveira
TrigNER: automatically optimized biomedical event trigger recognition on scientific documents. 1 - Luís Paquete
MOSAL: software tools for multiobjective sequence alignment. 2 - Bernard J. Pope
ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets. 3 - Matthew I. Bellgard
Correction: Dispelling myths about rare disease registry system development. 4 - Khadija Musayeva, Tristan Henderson
PFClust: an optimised implementation of a parameter-free clustering algorithm. 5 - Kuruvilla Abraham
Identifying large sets of unrelated individuals and unrelated markers. 6 - Jesus Herrera-Galeano, Kenneth G. Frey, Regina Z. Cer, Alfred J. Mateczun, Kimberly A. Bishop-Lilly, Vishwesh P. Mokashi:
BLASTPLOT: a PERL module to plot next generation sequencing NCBI-BLAST results. 7 - Chuming Chen
Software for pre-processing Illumina next-generation sequencing short read sequences. 8 - Richard A. Erickson
BatTool: an R package with GUI for assessing the effect of White-nose syndrome and other take events on Myotis spp. of bats. 9 - Moses P. Adoga
H3Africa: a tipping point for a revolution in bioinformatics, genomics and health research in Africa. 10 - Izaskun Mallona
Methylation plotter: a web tool for dynamic visualization of DNA methylation data. 11 - Neda Zamani, Görel Sundström, Marc P. Höppner, Manfred G. Grabherr
Modular and configurable optimal sequence alignment software: Cola. 12 - German Tischler, Steven Leonard:
biobambam: tools for read pair collation based algorithms on BAM files. 13 - Matthew I. Bellgard
Second generation registry framework. 14 - Daniel J. Park
Annokey: an annotation tool based on key term search of the NCBI Entrez Gene database. 15 - Guillaume Lamour
Easyworm: an open-source software tool to determine the mechanical properties of worm-like chains. 16 - Natapol Pornputtapong
A dedicated database system for handling multi-level data in systems biology. 17 - Michel Petitjean
VIRAPOPS2 supports the influenza virus reassortments. 18 - Aleksey A. Porollo
EC2KEGG: a command line tool for comparison of metabolic pathways. 19 - Harold R. Garner, Ashwin Puthige:
BioFlow: a web based workflow management software for design and execution of genomics pipelines. 20 - Christoph Wiedemann, Peter Bellstedt
PREdator: a python based GUI for data analysis, evaluation and fitting. 21 - Daniel A. Wagenaar
Publication quality 2D graphs with less manual effort due to explicit use of dual coordinate systems. 22 - Yong Xu, Fuquan Zhang
plot2groups: an R package to plot scatter points for two groups of values. 23 - David Keith Williams, Zoran Bursac
Three algorithms and SAS macros for estimating power and sample size for logistic models with one or more independent variables of interest in the presence of covariates. 24 - Mike Gavrielides, Simon J. Furney, Tim Yates, Crispin J. Miller, Richard Marais:
Onco-STS: a web-based Laboratory Information Management System for sample and analysis tracking in oncogenomic experiments. 25 - Robert V. Baron, Charles Kollar, Nandita Mukhopadhyay, Daniel E. Weeks:
Mega2: validated data-reformatting for linkage and association analyses. 26 - Thuy Nguyen, Kyungmin Song, Yury Tsoy, Jin Kim, Yong-Jun Kwon, Myungjoo Kang, Michael Edberg Hansen:
Robust dose-response curve estimation applied to high content screening data analysis. 27 - Héctor Echavarría-Heras, Cecilia Leal Ramírez, Enrique Villa-Diharce, Oscar Castillo:
Using the value of Lin's concordance correlation coefficient as a criterion for efficient estimation of areas of leaves of eelgrass from noisy digital images. 29 - Bohdan B. Khomtchouk, Derek J. Van Booven, Claes Wahlestedt:
HeatmapGenerator: high performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline. 30
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